Commit da8d1d1b authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry

Version numbering for everything

* Turned all '0.1dev' tool version numbers to '1.0.0'.
* Changed Stuttermark's version number from '1.5' to '1.5.0'.
* Added version numbers to the visualisations.
* Updated README.rst to include all tools, but removed the usage details
  of Stuttermark because it is highly impractical to include usage
  details for all tools in the README file. I'll leave that to the
  -h/--help option and the yet-to-write FDSTools User's Handbook.
parent e1bd3e41
......@@ -7,7 +7,7 @@ description of each tool, run:
``fdstools -h``
For a complete description of the command line arguments of a specific tool,
For a complete description of a specific tool and its command line arguments,
run:
``fdstools -h TOOLNAME``
......@@ -30,7 +30,29 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v0.0.3
- Includes Stuttermark v1.5
- Updated bundled JavaScript library Vega to v2.5.0
- Updated bundled JavaScript library D3 to v3.5.12
- Includes Allelefinder v1.0.0
- Includes BGCorrect v1.0.0
- Includes BGEstimate v1.0.0
- Includes BGHomRaw v1.0.0
- Includes BGHomStats v1.0.0
- Includes BGMerge v1.0.0
- Includes BGPredict v1.0.0
- Includes Blame v1.0.0
- Includes FindNewAlleles v1.0.0
- Includes Libconvert v1.0.0
- Includes Samplestats v1.0.0
- Includes Seqconvert v1.0.0
- Includes Stuttermark v1.5.0
- Includes Stuttermodel v1.0.0
- Includes TSSV v1.0.0
- Includes Vis v1.0.0
- Includes Allelevis v1.0.0beta1
- Includes BGRawvis v1.0.0
- Includes Profilevis v1.0.0
- Includes Samplevis v2.0.0
- Includes Stuttermodelvis v1.0.0beta1
v0.0.2
- Added global -d/--debug switch
......@@ -41,91 +63,157 @@ v0.0.1
- Includes Stuttermark v1.3
Stuttermark
-----------
Mark potential stutter products by assuming a fixed maximum percentage of
stutter product vs the parent allele.
Input
Tab-seperated file with the following columns:
- 'allele': the allele name, as a TSSV_-style sequence, e.g.,
"``AGAT(12)TGAT(4)``" (required)
- 'total': the total number of reads (required)
- 'name': the name of the marker (optional)
This format is compatible with 'knownalleles.csv' files created by TSSV_.
If raw sequences or allele names are provided, Stuttermark can convert
those to TSSV-style sequences automatically if a library file is given as
well.
Output
The same file, with an additional column (named 'annotation' by default).
The new column contains '``STUTTER``' for possible stutter products, or
'``ALLELE``' otherwise. Lines that were not evaluated are annotated as
'``UNKNOWN``'. The ``STUTTER`` annotation contains additional information.
For example,
``STUTTER:146.6x1(2-1):10.4x2(2-1x9-1)``
This is a stutter product for which at most 146.6 reads have come from the
first sequence in the output file ("``146.6x1``") and at most 10.4 reads
have come from the second sequence in the output file ("``10.4x2``"). This
sequence differs from the first sequence in the output file by a loss of
one repeat of the second repeat block ("``2-1``") and it differs from the
second sequence by the loss of one repeat in the second block *and* one
repeat in the ninth block ("``2-1x9-1``").
Changelog
Allelefinder
~~~~~~~~~~~~
v1.0.0
- Initial version
BGCorrect
~~~~~~~~~
v1.0.0
- Initial version
BGEstimate
~~~~~~~~~~
v1.0.0
- Initial version
BGHomRaw
~~~~~~~~
v1.0.0
- Initial version
BGHomStats
~~~~~~~~~~
v1.0.0
- Initial version
BGMerge
~~~~~~~
v1.0.0
- Initial version
BGPredict
~~~~~~~~~
v1.0.0
- Initial version
Blame
~~~~~
v1.0.0
- Initial version
FindNewAlleles
~~~~~~~~~~~~~~
v1.0.0
- Initial version
Libconvert
~~~~~~~~~~
v1.0.0
- Initial version
Samplestats
~~~~~~~~~~~
v1.0.0
- Initial version
Seqconvert
~~~~~~~~~~
v1.0.0
- Initial version
v1.5
Stuttermark
~~~~~~~~~~~
v1.5.0
- Changed column names 'name' and 'allele' to 'marker' and 'sequence',
respectively. WARNING: Stuttermark is now INCOMPATIBLE with output
from TSSV but made compatible with TSSV-Lite instead.
from TSSV_ but made compatible with TSSV-Lite and the new, bundled TSSV
tool instead.
v1.4
v1.4.0
- Stuttermark now accepts raw sequences and allele names as input, which
are automatically rewritten as TSSV-style sequences using a specified
library file
- The 'name' column is now optional
v1.3
v1.3.0
- First version of Stuttermark to be included in ``fdstools``
- Fixed crash that occurred when an empty allele (e.g., a primer dimer)
was encountered
- Stuttermark now prints a warning if an allele is encountered that is
not a TSSV_-style sequence
v1.2
v1.2.0
- All settings are now available from the command line
- Use 1-based indexing in ``STUTTER`` annotations
v1.1
v1.1.0
- Stuttermark now accepts file names and the minimum number of reads to
evaluate as command line arguments
v1.0
v1.0.0
- Initial version
Libconvert
----------
Stuttermodel
~~~~~~~~~~~~
v1.0.0
- Initial version
Convert between TSSV (tab-separated) and FDSTools (ini-style) library formats.
TSSV
~~~~
v1.0.0
- Initial version
Seqconvert
----------
Convert between raw sequences, TSSV-style sequences, and allele names.
Vis
~~~
v1.0.0
- Initial version
Allelefinder
------------
Allelevis
~~~~~~~~~
v1.0.0beta1
- Initial version
Find true alleles in a single-person reference sample.
BGRawvis
~~~~~~~~
v1.0.0
- Initial version
Profilevis
~~~~~~~~~~
v1.0.0
- Initial version
Samplevis
~~~~~~~~~
v2.0.0
- Initial version
Stuttermodelvis
~~~~~~~~~~~~~~~
v1.0.0beta1
- Initial version
.. _TSSV: https://pypi.python.org/pypi/tssv/
......@@ -21,7 +21,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files, \
ensure_sequence_format, get_sample_data, \
add_sequence_format_args
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -28,7 +28,7 @@ from ..lib import load_profiles, ensure_sequence_format, get_column_ids, \
nnls, add_sequence_format_args, SEQ_SPECIAL_VALUES, \
add_input_output_args, get_input_output_files
__version__ = "0.1dev"
__version__ = "1.0.0"
def get_sample_data(infile, convert_to_raw=False, library=None):
......
......@@ -17,7 +17,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
parse_allelelist, get_sample_data, \
add_random_subsampling_args
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -11,7 +11,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
add_allele_detection_args, parse_allelelist,\
get_sample_data, add_sequence_format_args
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -15,7 +15,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
get_sample_data, add_sequence_format_args, adjust_stats,\
add_random_subsampling_args
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -22,7 +22,7 @@ import sys
from ..lib import load_profiles, ensure_sequence_format,\
add_sequence_format_args
__version__ = "0.1dev"
__version__ = "1.0.0"
def merge_profiles(infiles, outfile, seqformat, library):
......
......@@ -31,7 +31,7 @@ from ..lib import get_column_ids, reverse_complement, get_repeat_pattern,\
mutate_sequence, SEQ_SPECIAL_VALUES,\
PAT_SEQ_RAW, ensure_sequence_format, add_sequence_format_args
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -19,7 +19,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
parse_allelelist, load_profiles, add_sequence_format_args,\
get_sample_data
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -12,7 +12,7 @@ from ..lib import ensure_sequence_format, add_sequence_format_args, \
get_column_ids, add_input_output_args, SEQ_SPECIAL_VALUES, \
get_input_output_files
__version__ = "0.1dev"
__version__ = "1.0.0"
def read_known(infile, library, default_marker=None):
......
......@@ -44,7 +44,7 @@ from ..lib import parse_library
from ConfigParser import RawConfigParser
from StringIO import StringIO
__version__ = "0.1dev"
__version__ = "1.0.0"
# If no input is given, convert the following to FDSTools format.
......
......@@ -33,7 +33,7 @@ import sys
from ..lib import add_sequence_format_args, add_input_output_args, \
get_input_output_files, get_column_ids
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -41,7 +41,7 @@ from ..lib import get_column_ids, ensure_sequence_format, parse_library,\
reverse_complement, add_input_output_args,\
get_input_output_files, SEQ_SPECIAL_VALUES
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -35,7 +35,7 @@ from ..lib import pos_int_arg, print_db, PAT_TSSV_BLOCK, get_column_ids, \
ensure_sequence_format, add_sequence_format_args, \
SEQ_SPECIAL_VALUES
__version__ = "1.5"
__version__ = "1.5.0"
# Default values for parameters are specified below.
......
......@@ -16,7 +16,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
add_random_subsampling_args, reverse_complement,\
get_repeat_pattern
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -19,7 +19,7 @@ from ..lib import pos_int_arg, add_input_output_args, get_input_output_files,\
add_sequence_format_args, reverse_complement, PAT_SEQ_RAW,\
get_column_ids
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
......@@ -34,7 +34,7 @@ from pkg_resources import resource_stream, resource_string
from ..lib import pos_int_arg
__version__ = "0.1dev"
__version__ = "1.0.0"
# Default values for parameters are specified below.
......
{
"fdstools_visversion": "1.0.0beta1",
"width": 600,
"height": 500,
"data": [
......
......@@ -4,6 +4,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="UTF-8">
<title>Allele Visualisation - FDSTools</title>
<!-- VERSION 1.0.0beta1 -->
<!-- BEGIN_LIBRARIES -->
<script src="http://vega.github.io/vega-editor/vendor/d3.min.js"></script>
<script src="http://vega.github.io/vega/vega.min.js"></script>
......
{
"fdstools_visversion": "1.0.0",
"width": 600,
"height": 10,
"signals": [
......
......@@ -4,6 +4,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="UTF-8">
<title>Background Noise Visualisation - FDSTools</title>
<!-- VERSION 1.0.0 -->
<!-- BEGIN_LIBRARIES -->
<script src="http://vega.github.io/vega-editor/vendor/d3.min.js"></script>
<script src="http://vega.github.io/vega/vega.min.js"></script>
......
......@@ -4,6 +4,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="UTF-8">
<title>Background Noise Profile Visualisation - FDSTools</title>
<!-- VERSION 1.0.0 -->
<!-- BEGIN_LIBRARIES -->
<script src="http://vega.github.io/vega-editor/vendor/d3.min.js"></script>
<script src="http://vega.github.io/vega/vega.min.js"></script>
......
{
"fdstools_visversion": "1.0.0",
"width": 600,
"height": 10,
"signals": [
......
......@@ -5,6 +5,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta charset="UTF-8">
<title>Sample Visualisation - FDSTools</title>
<!-- VERSION 2.0.0 -->
<!-- BEGIN_LIBRARIES -->
<script src="http://vega.github.io/vega-editor/vendor/d3.min.js"></script>
<script src="http://vega.github.io/vega/vega.min.js"></script>
......
{
"fdstools_visversion": "2.0.0",
"width": 600,
"height": 10,
"signals": [
......
......@@ -4,6 +4,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="UTF-8">
<title>Stutter Model Visualisation - FDSTools</title>
<!-- VERSION 1.0.0beta1 -->
<!-- BEGIN_LIBRARIES -->
<script src="http://vega.github.io/vega-editor/vendor/d3.min.js"></script>
<script src="http://vega.github.io/vega/vega.min.js"></script>
......
{
"fdstools_visversion": "1.0.0beta1",
"width": 600,
"height": 10,
"signals": [
......
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